Variant report

Variant	rs2128172
Chromosome Location	chr15:56941323-56941324
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56932749..56935204-chr15:56940606..56943085,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TEX9-4	chr15:56940274-56941388	ucscGeneNc_uc002afm_2

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10518858	0.86[EUR][1000 genomes]
rs11071282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11071283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634704	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11635201	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12148781	0.87[EUR][1000 genomes]
rs12441674	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1600830	0.84[EUR][1000 genomes]
rs1680488	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28374324	0.88[EUR][1000 genomes]
rs28379958	0.87[EUR][1000 genomes]
rs28409651	0.89[EUR][1000 genomes]
rs28441487	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28510121	0.84[AFR][1000 genomes]
rs28620046	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28678122	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28778716	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28782544	0.88[EUR][1000 genomes]
rs28805712	0.88[EUR][1000 genomes]
rs28813195	0.88[EUR][1000 genomes]
rs28830569	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28842489	0.87[EUR][1000 genomes]
rs28893316	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774870	0.88[EUR][1000 genomes]
rs4774876	0.87[EUR][1000 genomes]
rs4774881	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4774891	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs534005	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs56327619	0.86[EUR][1000 genomes]
rs7164084	0.91[YRI][hapmap]
rs7182346	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs72744943	0.88[AFR][1000 genomes]
rs72744954	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744977	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs8026706	0.88[EUR][1000 genomes]
rs8031549	0.88[EUR][1000 genomes]
rs8031966	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8032893	0.88[EUR][1000 genomes]
rs809459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9806469	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1041239	chr15:56888945-56959028	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56902800-56945400	Weak transcription	Right Ventricle	heart
2	chr15:56910600-56945400	Weak transcription	HSMMtube	muscle
3	chr15:56912800-56957000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr15:56913400-56955200	Weak transcription	Aorta	Aorta
5	chr15:56916600-56990800	Weak transcription	Pancreas	Pancrea
6	chr15:56916800-56949800	Weak transcription	Fetal Kidney	kidney
7	chr15:56917200-56955200	Weak transcription	Psoas Muscle	Psoas
8	chr15:56917600-56944800	Weak transcription	Fetal Brain Male	brain
9	chr15:56917600-56957000	Weak transcription	Brain Anterior Caudate	brain
10	chr15:56917800-56945400	Weak transcription	GM12878-XiMat	blood
11	chr15:56917800-56955800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:56917800-56956800	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:56917800-56959800	Weak transcription	Brain Angular Gyrus	brain
14	chr15:56917800-56990600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr15:56917800-56990600	Weak transcription	NHLF	lung
16	chr15:56918000-56945200	Weak transcription	A549	lung
17	chr15:56918000-56945600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:56918400-56945400	Weak transcription	Fetal Intestine Small	intestine
19	chr15:56918400-56957200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:56919600-56955200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
22	chr15:56920000-56945400	Weak transcription	Fetal Intestine Large	intestine
23	chr15:56920000-56953000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:56920400-56945400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr15:56921600-56955200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:56921600-56955400	Weak transcription	NH-A	brain
27	chr15:56922000-56954800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:56922000-56958000	Weak transcription	Lung	lung
29	chr15:56922200-56945400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:56922400-56945400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:56922800-56945400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr15:56924000-56945400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:56924000-56945400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:56924000-56990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:56924000-56990800	Weak transcription	NHEK	skin
36	chr15:56924200-56944800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr15:56924200-56945400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:56924200-56945400	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:56924200-56945400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:56924200-56945400	Weak transcription	Fetal Lung	lung
41	chr15:56924200-56945400	Weak transcription	Left Ventricle	heart
42	chr15:56924200-56949000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:56924200-56955400	Weak transcription	Fetal Brain Female	brain
44	chr15:56924600-56945400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:56924600-56957200	Weak transcription	HUVEC	blood vessel
46	chr15:56925200-56942400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:56928400-56996800	Weak transcription	Gastric	stomach
48	chr15:56930000-56945400	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:56930000-56950000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:56930000-56954800	Weak transcription	Fetal Stomach	stomach

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